Publications of NIPGR Scientists
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Item UFMylation: Exploring a lesser known post translational modification(Elsevier B.V., 2025) Sharma, Rohit; Chirom, Oceania; Mujib, Abdul; Prasad, Manoj; Prasad, AshishUbiquitination is a highly conserved post-translational modification (PTM) in which ubiquitin (Ub) is covalently attached to substrate proteins resulting in the alteration of protein structure, function, and stability. Another class of PTM mediated by ubiquitin-like proteins (UBLs) has gained significant attention among researchers in recent years. This article focuses on one such UBL-mediated PTM i.e. UFMylation. The enzymatic mechanism of UFMylation is similar to ubiquitination, involving three steps regulated by three different enzymes. In plants, reports suggest that UFMylation is predominantly involved in maintaining ER homeostasis including ER-phagy. However, studies related to this PTM are limited and future studies might reveal other molecular pathways regulated by UFMylation.Item Catalase regulation during plant-virus-vector interaction(John Wiley & Sons, 2024) Sharma, Rohit; Pandey, Saurabh; Prasad, Manoj; Prasad, AshishPlant-virus-host interaction is a complex process involving several players. A constant arms race between the hosts and viruses has led to their co-evolution. Reactive oxygen species (ROS) are important signaling molecules that regulate plant growth, development, and stress responses. Barley yellow dwarf virus (BYDV) has a wide host range and infects several plant species such as barley, rice, oats, wheat, etc. A recent study by Tian et al. (2024) has highlighted that the movement protein (MP) of BYDV is involved in manipulation of the host ROS pathway to promote viral multiplication as well as transmission. The findings display the multifaceted role of a viral protein that is otherwise involved in movement. The limited coding ability of viruses is compensated by their proteins having multiple roles in the modulation of several different host molecular pathways. This is one of the key reasons for viruses being successful pathogens despite their limited coding ability.Item Deeper look into viruses: replication intermediates do code!(Springer Nature Publishing AG, 2024) Prasad, Ashish; Sharma, Shambhavi; Prasad, ManojIt is quite intriguing how viruses with their limited coding ability are able to infect their hosts. Processes like RNA editing, transcriptional slippage, RNA splicing, programmed ribosome frameshifting, ribosomal leaky scanning, translational initiation from non-AUG codons, alternative splicing and several other mechanisms greatly expand the coding capacity of viruses, resulting in a more diverse transcriptome and proteome which is conventionally predicted from the ORFs (Ho et al. 2021). Several studies have highlighted that viruses encode various small ORFs that play important roles in viral lifecycle and infection (Gong et al. 2021; Shi et al. 2023). Positive-sense single-stranded RNA (+ ssRNA) viruses have a RNA genome that can act as mRNA and can be translated directly (Louten 2016). These viruses synthesize an −RNA strand which has been long believed to be a replication intermediate without coding ability that serves as a template for synthesizing more + ssRNA strands. However, some studies have highlighted that −RNA replication intermediates do have coding ability expanding the transcriptome of such viruses (Dinan et al. 2020; Retallack et al. 2021; Zhang et al. 2023; Gong et al. 2023).Item Selective autophagy: the fulcrum of plant-virus interaction(Elsevier B.V., 2024) Sharma, Shambhavi; Prasad, Ashish; Prasad, ManojSelective autophagy receptors play both proviral and antiviral roles during plant-virus interaction. However, little is known about the balance between such contradictory dual roles of these receptors. Tong et al. have deciphered the temporal regulation of antiviral and antiplant roles of a selective autophagy receptor, a virus-induced small peptide 1 (VISP1).Item Post translational modifications at the verge of plant-geminivirus interaction(Elsevier B.V., 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, ManojPlant-virus interaction is a complex phenomenon and involves the communication between plant and viral factors. Viruses have very limited coding ability yet, they are able to cause infection which results in huge agro-economic losses throughout the globe each year. Post-translational modifications (PTMs) are covalent modifications of proteins that have a drastic effect on their conformation, stability and function. Like the host proteins, geminiviral proteins are also subject to PTMs and these modifications greatly expand the diversity of their functions. Additionally, these viral proteins can also interact with the components of PTM pathways and modulate them. Several studies have highlighted the importance of PTMs such as phosphorylation, ubiquitination, SUMOylation, myristoylation, S-acylation, acetylation and methylation in plant-geminivirus interaction. PTMs also regulate epigenetic modifications during geminivirus infection which determines viral gene expression. In this review, we have summarized the role of PTMs in regulating geminiviral protein function, influence of PTMs on viral gene expression and how geminiviral proteins interact with the components of PTM pathways to modulate their function.Item Multihost compatibility of Fusarium oxysporum: early root colonization effectors into the action!(Springer Nature Publishing AG, 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, ManojAgricultural productivity is greatly afected by several biotic factors which include insects, nematodes, bacteria, fungi, and viruses. Fungal pathogens in particular are a major setback to optimum crop production. A fungal species causing huge agro-economic losses world-wide is the Fusarium oxysporum (Fo) species complex. Fo is known to cause cross-kingdom infections in plants and humans (Zhang et al. 2020). In plants, it causes vascular wilt in several species; however, any particular Fo formae speciales (Fo f. sp.) can cause symptomatic infection on one or a few related species by invading their vasculature. Some important Fo f. sp. include apii, conglutinans, cubense, lycopersici, and melongena (Arie 2019). These strains can also survive in the root cortex of other hosts without invading the vasculature resulting in asymptomatic root colonization. A study by Redkar et al. has revealed that such an endophytic growth in multiple hosts is regulated by a group of conserved fungal efectors known as early root colonization (ERC) efectors.Item Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction(Elsevier B.V., 2023) Sharma, Shambhavi; Sett, Susmita; Das, Tuhin; Prasad, Ashish; Prasad, ManojIn natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.Item Suppressing plant defence: Scavenge the ROS!(John Wiley & Sons, 2023) Prasad, Ashish; Sharma, Shambhavi; Prasad, ManojROS-mediated defence against fungal pathogens is an essential arm of plant immunity. As a counter defence, these pathogens synthesize antioxidant enzymes that scavenge the ROS produced by plants. The molecular mechanism behind the upregulation of these enzymes in fungal pathogens was unknown. A recent study by Zhang and colleagues has shed light on the mechanism, and it has been shown that deacetylation of FolSrpk1 protein on the K304 residue following oxidative stress is an important event in the signalling cascade leading to ROS detoxification in Fusarium oxysporum f. sp. lycopersici. Deacetylated FolSrpk1 moves to the nucleus where it hyperphosphorylates FolSr1, which further regulates the transcription of antioxidant enzymes (Zhang et al. 2023). This mechanism of ROS detoxification is conserved in Botrytis cinerea as well. Several other phytopathogenic fungi have a corresponding K304 site and NLS present in their Srpk1, suggesting a similar mechanism of ROS detoxification and suppression of plant defence. In this article, we have presented our views on how future studies can be synthesized based on the pathway deciphered by Zhang et al. 2023.Item Ubiquitination from the perspective of plant pathogens(Oxford University Press, 2023) Sharma, Shambhavi; Prasad, Ashish; Prasad, ManojThe constant battle of survival between pathogens and host plants has played a crucial role in shaping the course of their co-evolution. However, the major determinants of the outcome of this ongoing arms race are the effectors secreted by pathogens into the host cells. These effectors perturb the defense responses of plants to promote their successful infection. In recent years, the extensive research in the area of effector biology has reported an increase in the repertoire of pathogenic effectors that mimics or targets the conserved ubiquitin proteasomal pathway. The role of ubiquitin mediated degradation pathway has been well known to be indispensable for various aspects of plant’s life, thus targeting or mimicking it seems to be a smart strategy adopted by pathogens in their favor. Therefore, this review summarizes the recent findings on how some pathogenic effectors mimics or act as one of the components of ubiquitin proteasomal machinery while others directly target the plant’s ubiquitin proteasomal system.Item Osmosensing in plants: mystery unveiled(Elsevier B.V., 2023) Sharma, Shambhavi; Prasad, Ashish; Prasad, ManojOsmotic stress limits plant growth and productivity. The downstream signaling components involved in osmotic adjustments are well known, but our knowledge of the perception of osmotic stress is far too limited. Wang et al. have recently identified a lesser-known mechanism of bimolecular condensation that underlies osmotic stress perception in plants.